The determination of free ammonia in ambient air with diffusion/denuder tubes

Ammonia is important in atmospheric chemistry because it neutralises acidic species and increases the pH of cloud droplets. Data on the concentration of free ammonia in the atmosphere are sparse because it is difficult to separate free ammonia from particulate ammonium salt aerosol. A manual method for the determination of free ammonia in air is described based on diffusion/denuder tube separation of ammonia from ammonium salt aerosol. When air is drawn through a tube coated with a selective absorbent (here oxalic acid) separation is achieved because the gaseous species diffuses much more rapidly to the tube wall than the particles. After the sampling period (usually 1–4 h, depending on the free ammonia concentration expected), the sorbed ammonia is washed from the tube and measured potentiometrically with an ammonia probe. The method is tested theoretically and experimentally. The absorption efficiency of the coated tubes is ca. 90%. In samples of room air containing 12–28 μg m^?3, the standard deviation is estimated as 1.0 μg m^?3. In field use, ammonia contents were in the range 0.53–5.0 μg m^?3.     

Experimental evidence for a general model of modulated MOF nanoparticle growth

Nanoparticles of metal–organic frameworks (nanoMOFs) boast superior properties compared to their bulk analogs, yet little is known about how common synthetic parameters dictate particle sizes. Here, we provide experimental evidence for the “seesaw” model of nanoMOF growth. Solution acidity, ligand excess, and reactant concentrations are decoupled and shown to form the key independent determinants of nanoMOF sizes, thereby validating the proposal that nanoMOFs arise from coupled equilibria involving ligand deprotonation and metal–ligand complexation. By achieving the first demonstration of a seesaw relationship between nanoMOF sizes and ligand excess, these results provide further proof of the model, as they required deliberate manipulation of relationships outlined by the model. Exploring the relative impacts of these parameters reveals that ligand excess has the greatest ability to decrease sizes, although low acidity and high concentrations can exhibit similar effects. As a complement to existing models of polymer formation and crystal growth, the seesaw model therefore offers a powerful tool for reliable control over nanoMOF sizes.

Nanoparticles of metal–organic frameworks (nanoMOFs) boast superior properties compared to their bulk analogs, yet little is known about how common synthetic parameters dictate particle sizes.     

Mechanism of the oxidation of L-ascorbic acid by the bis(pyridine-2,6-dicarboxylate)cobaltate(III) ion in aqueous solution

A detailed investigation of the oxidation of L-ascorbic acid (H₂A) by the title complex has been carried out using conventional spectrophotometry at 510 nm, over the ranges: 0.010 [ascorbate] _T 0.045 mol dm^–3, 3.62 pH 5.34, and 12.0 30.0 °C, 0.50 I 1.00 mol dm^–3, and at ionic strength 0.60 mol dm^–3 (NaClO₄). The main reaction products are the bis(pyridine-2,6-dicarboxylate)cobaltate(II) ion and l-dehydroascorbic acid. The reaction rate is dependent on pH and the total ascorbate concentration in a complex manner, i.e., k _obs = (k ₁ K ₁)[ascorbate] _T /(K ₁ + [H⁺]). The second order rate constant, k ₁ [rate constant for the reaction of the cobalt(III) complex and HA^–] at 25.0 °C is 2.31 ± 0.13 mol^–1 dm³ s^–1. H = 30 ± 4 kJ mol^–1 and S = –138 ± 13 J mol^–1 K^–1. K ₁, the dissociation constant for H₂A, was determined as 1.58 × 10^–4 mol dm^–3 at an ionic strength of 0.60 mol dm^–3, while the self exchange rate constant, k ₁₁ for the title complex, was determined as 1.28 × 10^–5 dm³ mol^–1 s^–1. An outer-sphere electron transfer mechanism has been proposed.     

Nucleic acid analysis using an expanded genetic alphabet to quench fluorescence

Organic chemistry has made possible the synthesis of molecules that expand on Nature's genetic alphabet. Using the previously described nonstandard DNA base pair constructed from isoguanine and 5-methylisocytosine, we report a highly specific and sensitive method that allows for the fast and specific quantitation of genetic sequences in a closed tube format. During PCR amplification, enzymatic site-specific incorporation of a quencher covalently linked to isoguanine allows for the simultaneous detection and identification of multiple targets. The specificity of method is then established by analysis of thermal denaturation or melting of the amplicons. The appropriate functions of all reactions are further verified by incorporation of an independent target into the reaction mixture. We report that the method is sensitive down to the single copy level, and specificity is demonstrated by multiplexed end-point genotypic analysis of four targets simultaneously using four separate fluorescent reporters. The method is general enough for quantitative and qualitative analysis of both RNA and DNA using previously developed primer sets. Though the method described employs the commonly used PCR, the enzymatic incorporation of reporter groups into DNA site-specifically should find broad utility throughout molecular biology.     

Infrared spectroscopic studies of polystyrene emulsion polymers: Effect of oxidation during polymerization

Infrared spectroscopy was empolyed to study the nature of the structural changes which occurred through oxidation during the emulsion polymerization of styrene. Aliphatic carboxylic, amino, and phosphate emulsifiers and hydrogen peroxide and potassium persulfate initiators were empolyed for polymer preparation. In addition, a polystyrene dispersion prepared in the absence of any emulsifier or stabilizer was examined. Irrespective of the nature of the initiator–emulsifier combination employed, all of the polymer spectra revealed bands at 1705 and 1770 cm.^?1. The band at 1705 cm.^?1 was assigned in part to the carbonyl stretching mode of dimertic carboxylic acid, formed by oxidation, in the polystyrene chains. Absorption at 1770 cm.^?1, which was very weak, was tentatively attributed to the carbonyl stretching mode of the monomeric form of this acid. The structure of the acid endgroup was not established, but the results obtained suggest that it was possibly a phenylacetic acid residue or a residue with a similar structure.     

Hexafluorothioacetone based synthesis of fluorinated heterocycles

Cycloadducts of hexafluorothioacetone (HFTA) were prepared in high yield by a CsF catalyzed reaction between readily available 2,2,4,4-tetrakis-(trifluoromethyl)-1,3-dithietane (as a source of HFTA) with conjugated electron-rich hydrocarbon dienes, such as cyclopentadiene, 2,3-dimethylbuta-1,3-diene, cyclohexa-1,3-diene or (1Z,3Z)-cyclohepta-1,3-diene. Cyclohexa-1,4- and (1Z,5Z)-cycloocta-1,5-dienes, also undergo the reaction with in situ generated HFTA, but form the products of insertion of HFTA into the C-H bond of the diene as a result of ene-reaction. The highly selective reaction of HFTA with (1Z,3Z,5Z)-cyclohepta-1,3,5-triene and (1Z,3Z,5Z,7Z)-cycloocta-1,3,5,7-tetraene leads to the formation of cycloadducts derived from exclusive addition of thioacetone to the corresponding bicyclic isomers—bicyclo[4.1.0]hepta-2,4-diene or bicyclo[4.2.0]octa-2,4,7-triene, respectively. The corresponding cycloadducts of HFTA with 2,3-dimethylbutadiene-1,3-cyclohexa-1,3-cyclohexa-1,4-dienes and (1Z,3Z,5Z)-cyclohepta-1,3,5-triene were also prepared by direct reaction of sulfur/hexafluoropropene/KF and the corresponding hydrocarbon substrate at 35-45 °C in DMF.     

Rapid and sensitive identification of epitope-containing peptides by direct matrix-assisted laser desorption/ionization tandem mass spectrometry of peptides affinity-bound to antibody beads

A method has been developed for rapid and sensitive identification of epitope-containing peptides, based on direct MALDI-MS/MS analysis of epitope-containing peptides affinity bound to affinity beads. This technique provides sequence information of the epitope that allows unambiguous identification of the epitope either by database searching or de novo sequencing. With MALDI-MS, affinity beads with bound peptides can be placed directly on the MALDI target and analyzed. Coupling a MALDI source to an orthogonal injection quadrupole time-of-flight (QqTOF) mass spectrometer allows direct sequencing of the bound peptides. In contrast to ESI-MS/MS, elution of the affinity-bound peptides followed by additional concentration and purification steps is not required, thus reducing the potential for sample loss. Direct mass spectrometric sequencing of affinity-bound peptides eliminates the need for chemical or enzymatic sequencing. Other advantages of this direct MALDI-MS/MS analysis of epitope-containing peptides bound to the affinity beads include its sensitivity (femtomole levels) and speed. In addition, direct analysis of peptides on affinity beads does not adversely affect the high mass accuracy of a QqTOF, and database searching can be performed on the MS/MS spectra obtained. In proof-of-principle experiments, this method has been demonstrated on beads containing immobilized antibodies against phosphotyrosine, the c-myc epitope tag, as well as immobilized avidin. Furthermore, de novo sequencing of epitope-containing peptides is demonstrated. The first application of this method was with anti-FLAG-tag affinity beads, where direct MALDI MS/MS was used to determine an unexpected enzymatic cleavage site on a growth factor protein.     

Synthesis of the C6-C21 segment of amphidinolide E

[reaction: see text] A convergent approach to a C6-C21 segment of the polyketide amphidinolide E has been developed through combination of three subunits by allenylindium bromide-aldehyde addition and Suzuki sp2-sp3 coupling.     

Comparison of mass resolution criteria in mass spectrometry

For a single peak, mass spectral resolution can be expressed in terms of peak width or ratio of peak position to peak width. Alternatively, for two equally intense peaks of equal width, resolution can be defined as the minimum peak separation such that the height of the valley between the combined peaks is less than a specified ratio (1%, 10%, 50%, 100%) of the individual (or combined) peak maximum. All these definitions depend on peak shape. Conversion formulae between various mass resolution criteria are presented for each of eight spectral peak shapes: Gaussian, triangular, trapezoidal, Lorentzian (absorption-mode, magnitude-mode, and sine-apodized magnitude-mode), and sinc (absorption-mode and magnitude-mode). From these formulae, mass resolutions based upon different criteria are readily compared for the same or different line shapes.     

Pseudo-MS3 in a MALDI orthogonal quadrupole-time of flight mass spectrometer

Both the matrix selected and the laser fluence play important roles in MALDI-quadrupole/time of flight (QqTOF) fragmentation processes. "Hot" matrices, such as alpha-cyano4-hydroxycinnamic acid (HCCA), can increase fragmentation in MS spectra. Higher laser fluence also increases fragmentation. Typical peptide fragment ions observed in the QqTOF are a, b, and y ion series, which resemble low-energy CID product ions. This fragmentation may occur in the high-pressure region before the first mass-analyzing quadrupole. Fragment ions can be selected by the first quadrupole (Q1), and further sequenced by conventional MS/MS. This allows pseudo-MS3 experiments to be performed. For peptides of higher molecular weight, pseudo-MS3 can extend the mass range beyond what is usually accessible for sequencing, by allowing one to sequence a fragment ion of lower molecular weight instead of the full-length peptide. Peptides that predominantly show a single product ion after MS/MS yield improved sequence information when this technique is applied. This method was applied to the analysis of an in vitro phosphorylated peptide, where the intact enzymatically-generated peptide showed poor dissociation via MS/MS. Sequencing a fragment ion from the phosphopeptide enabled the phosphorylation site to be unambiguously determined.